[Chimera-users] [chimerax-users] Automate calculation and saving of residues' structural attributes

Fri Feb 4 00:52:02 PST 2022

Hi Elaine,

the benchmarking is in principle the code of Andre and I, vs. the
caluclation performed by chimera. And this includes also the xyzr
conversion. 

And thank you for the information regarding the VDW radii. I will check
these values and compare them to the msms provided data. But I am pretty
sure, that we will find the key here for the differences we observe.

Thanks a lot.

Best
Christian

>>> Elaine Meng <meng at cgl.ucsf.edu> 02/03/22 7:47 PM >>>
Hi Christian,
I guess this is a Chimera question now, so I set the "reply to" to
chimera-users in case this generates further messages.  The following
pertains to Chimera.  

I believe it uses the MSMS code without modification to do the actual
calculation, so it might be needless work to run all this benchmarking. 
Nevertheless I can understand why you want to figure out the cause of
any differences.

(a) I would expect differences in VDW radii to be a major factor.  The
Chimera default radii are described/listed in the User Guide, see this
and links therein:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html>

You could try assigning the MSMS-provided radii within Chimera before
performing the area calculation in Chimera.  See the bottom section of
the help page URL above for possible ways of assigning different VDW
radius values.

(b) secondarily, it depends how you use the command... if you just used
Chimera command "surface" it would automatically just surface the
macromolecules and try to omit waters, ligands, etc.  However, you can
use "surfcat" command to define whatever sets of atoms you like for
subsequent "surface" calculations.
Chimera surface command
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html>
Chimera surfcat command
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>

(c) dealing with the code is beyond my skill set, so if you still need
pointers to look therein, somebody else would have to advise.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 3, 2022, at 12:33 AM, Christian Tüting via ChimeraX-users
<chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi All,
> 
> Andre and I continued this conversation in private, as this was not
> Chimera related anymore.
> 
> Somehow, we have a question regarding the calculation of the of the
SES
> and SAS. 
> 
> In principle, I looked into the calcsurf.py file in the chimera
folder,
> and figured out, that this calculation is done by msms with a probe
> radius of 1.4 and a density of 2 and noh. So I copied the code into my
> workflow and tested this with a xyzr file, generated by the
pdb_to_xyzr
> shell script from msms, and got the same results, as if I am running
> directly msms from command line. So far not suprisingly.
> 
> But when we take the same pdb file, the msms code itself gives
slightly
> different values than chimera. Often, it's not siginificant, but Andre
> benchmarked this, and sometimes the difference is more than 1.2 fold.
> 
> 
> 
> So this let us come to the conclusion, that chimera somehow calculates
a
> different xyzr file, compared to what the shell script is doing. I was
> not able to find the code for caluclating the xyzr file. Another
> explanation is, that chimera treats the results a bit differently.
msms
> results ses and sas per atom, we "just" summed them per residue to get
> the per residue value. But I don't think, that this is done
differently
> here.
> 
> 
> So our questions are:
> (a) is the radius definition different in chimera from what is given
> with the msms software ( https://ccsb.scripps.edu/msms/downloads/;
there
> is a shellscript and, more importantly a text file, which defines the
> radius of each atom, with a lot of special cases ).
> (b) is the structure somehow "filtered" prior to surface calculation.
> E.g. are waters, ions, ligands considered part of the structure, of> (c) or can you help us find the actual code for this in chimera, than
I
> will be able to anwser the question myself
> 
> Thanks in advance.
> 
> Christian
> 
> 
> 
>>>> André <andre.jfmdm at gmail.com> 01/21/22 7:06 PM >>>
> Hi Elaine,
> 
> Thank you so much for your very helpful answer!
> 
> Yeah, Tom told me before that it wouldn't be possible to directly
> calculate
> SESA and relSESA with ChimeraX. So, I'll probably have to stick with
> Chimera. I've just discovered the "list" command (functional in
> Chimera),
> and I think that with it I'll be able to easily get all the attributes
> by
> using the --nogui startup.
> I'll work on it in the following days, then I'll come back with
updates.
> 
> Once again, thank you very much!
> 
> Best,
> André.
> 
> Em sex., 21 de jan. de 2022 às 13:55, Elaine Meng <meng at cgl.ucsf.edu>
> escreveu:
> 
>> Hi André,
>> Although it displays an SES, ChimeraX does not calculate SES areas,
> only
>> SAS areas (command "measure sasa" which also assigns a residue
> attribute).
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa>
>> 
>> For Chimera, another group had provided SES reference areas for the
>> exposed state represented by G-X-G tripeptides, but I don't know of a
>> similar SAS reference area set for ChimeraX that could be used to
> calculate
>> relative exposure, sorry.  In case others are interested, the Chimera
>> relative exposure calculation giving relSESA is described here:
>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html>
>> 
>> So depending on the importance of SESA and relSESA, you may need to
> use
>> Chimera, or at least some method outside of ChimeraX.
>> 
>> In both ChimeraX and Chimera, bfactor is read from the input PDB
file,
> and
>> phi and psi are calculated automatically for peptide/protein
> structures
>> when they are read in.  ChimeraX atom and residue attributes:
>> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#atom>
>> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>
>> 
>> kdHydrophobicity is not a calculation, but a simple lookup table by
> amino
>> acid type.  You may not need either program to "calculate" it, but it
> is
>> automatically assigned in Chimera.  It can be assigned in ChimeraX by
>> running this comand script:
>> <
>> 
> https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle> values along
with some alternative hydrophobicity scales (lookup
> tables)
>> are summarized here:
>> 
>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Jan 21, 2022, at 7:28 AM, André via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Christian,
>>> 
>>> Thank you so much for your solution! That indeed helps a lot, since
> it
>> shows me how to execute ChimeraX scripts independently and directly
> from
>> Python!
>>> 
>>> Now, do you know which commands I should use to calculate the
> following
>> structural attributes for all residues: areaSAS, areaSES, relSESA,
> bfactor,
>> kdhydro, phi, psi?
>>> 
>>> I do it manually in Chimera (haven't figured out how to do the same
> in
>> ChimeraX yet), by following the route: Tools -> Structure Analysis ->
>> Render by Attribute -> File -> Save Attributes -> Attribute to Save,
> which
>> allows each attribute of residues to be saved as txt files, which
> contain
>> the residue number and respective attribute, for all residues in the
>> protein. For example, the file for areaSAS looks like this:
>>> 
>>> attribute: areaSAS
>>> recipient: residues
>>> :1.B 116.71626508235931
>>> :2.B 118.39353680610657
>>> ...
>>> 
>>> Thus, that's what I wanted to do: figure out which commands I should
> use
>> to get the same result as the manual route above (although it  is not
>> really necessary that the txt file> example
>> you showed, I'd be able to parse it to a file, and the problem would
> be
>> solved!).
>>> 
>>> Once again, thank you for your help!
>>> 
>>> Best,
>>> André.
>>> 
>>> 
>>> 
>>> Em sex., 21 de jan. de 2022 às 09:56, Christian Tüting <
>> christian.tueting at biochemtech.uni-halle.de> escreveu:
>>> Hi André,
>>> 
>>> i am pretty sure, that my solution is very crude and that there are
>>> better ways of doing it (like importing chimerax in the python code
>>> directly). I guess, you'll get more anwsers soon.
>>> 
>>> I quickly wrote a script, which performs a chimerax task
> independently,
>>> by just running python code.
>>> 
>>> First: a chimerax script file with the desired commands:
>>> 
>>> script.cxc:
>>> open 7ott
>>> surface #1
>>> mearuse area #1
>>> exit
>>> 
>>> Note: the exit command is needed, otherwise the subprocress will
> idle in
>>> the chimerax cmd line.
>>> 
>>> 
>>> Second: a python script, which execute this script in chimerax and
>>> fetches the output:
>>> 
>>> test.py:
>>> 
>>> import subprocess
>>> import os
>>> 
>>> cwd = os.getcwd()
>>> 
>>> chimerax =
> "/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX"
>>> scriptfile = f"{cwd}/script.cxc"
>>> 
>>> cmd = [chimerax, "--nogui",scriptfile]
>>> p = subprocess.run(" ".join(cmd),shell = True,capture_output=True)
>>> 
>>> stdout_as_str = p.stdout.decode("utf-8")
>>> print(stdout_as_str)
>>> 
>>> This just runs a subprocess and fetches the output to a string,
> which
>>> you can than further analyse.
>>> 
>>> 
>>> Best
>>> Christian
>>> 
>>> 
>>> 
>>> Dr. rer. nat. Christian Tüting
>>> 
>>> Kastritis Laboratory for Biomolecular Research
>>> Cryo-Electron Microscopy & Computational Structural Biology
>>> ________________________________________________
>>> Martin-Luther-Universität Halle-Wittenberg
>>> Biozentrum, Room A.2.19
>>> IWE ZIK HALOmem NWG III
>>> "Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
>>> Weinbergweg 22, 06120 Halle
>>> tel: +49 345 5524985
>>> web (Lab): https://blogs.urz.uni-halle.de/kastritislab/
>>> web (HALOmem): https://www.halomem.de/en/
>>>>>> André via ChimeraX-users <chimerax-users at cgl.ucsf.edu> 01/21/22
> 1:29
>>> PM >>>
>>> Hello!
>>> 
>>> I'm working on an automated pipeline (in Python) for the structural
>>> analysis of proteins. In particular, I'm using Chimera to> >
areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the
>>> inputs
>>> of the pipeline.
>>> However, currently the files are exported manually, and, for the
> purpose
>>> of
>>> building a fully automated pipeline, it would be great to also
> automate
>>> this step of calculating the attributes and exporting their
> respective
>>> files.
>>> 
>>> I searched a lot, and tried some ways to achieve such an automation
>>> (using
>>> Chimera), but nothing worked.
>>> And I also considered using ChimeraX. In particular, I went through
>>> ChimeraX Programming Manual (
>>> https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html#), but, if I
>>> understood correctly, I'd only be able to import chimerax and use
> its
>>> functions in the Python interpreter within ChimeraX (Tools >>
> General >>
>>> Shell).
>>> At first, I'd like to import chimerax as a module in a Python
>>> interpreter
>>> outside of ChimeraX, so that manually opening ChimeraX wouldn't be
>>> necessary in order to save the files with the residues' attributes.
> But,
>>> from some other threads in the mailing list, I found that it
> wouldn't be
>>> possible (right?)
>>> 
>>> But I also found out that I could write a .py script which
> calculates
>>> and
>>> exports the files with the residues' properties, and then run it
> with
>>> ChimeraX application from the command-line, something like:
> *chimerax
>>> --nogui myscript.py*
>>> If that works, I think that my automation problem would be solved!
> The
>>> only
>>> problem is that I really couldn't figure out the Python code to
>>> calculate
>>> and export the aforementioned residues' >>> find what I need, nor more detailed documentation).
>>> 
>>> Given that, I'd like to know if anyone has done something like this,
>>> and/or
>>> have any guidance on how I could proceed.
>>> 
>>> I really appreciate any help you can provide!
>>> (And thanks to Tom Goddard for suggesting moving the discussion here
> to
>>> the
>>> ChimeraX mailing list).
>>> 
>>> Thank you so much,
>>> André.
>>> 
>>> _______________________________________________
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>>> ChimeraX-users at cgl.ucsf.edu
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>> 
>> 
> 
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